VIRUSES, BACTERIA, ARCHAEA and PROTIST

Viruses• Virus = (Latin) Poison• Viruses are NOT considered to be living.• do not metabolize, respond to environment, or

reproduce on their own.• Viruses are NOT cells.• no nucleus, organelles, or cytoplasm

• Do have features in common with life• Have genetic material (DNA or RNA)• Evolve

Viruses• Extreme genetic diversity of viruses

suggest they do not have a single common ancestor

• Not part of any domain or kingdom• Viruses assigned species, genera, and

families but no taxonomy higher than order

• All viruses:• Contain genetic material (DNA or RNA)• Have a protein coat (Capsid)

Viruses• Tiny, infectious agents that:• have a nucleic acid core (RNA or DNA, but not

both).• have a protein coat (capsid) made of capsomers.• may have a lipid rich envelope.• This structural unit is called a virion (a single viral

particle).

Envelope• Viral envelope is composed of lipids

carbohydrates & proteins which is derived from the host.

• Proteins are what allow for attachment to host. • Enveloped viruses need envelope to initiate

infection.HIV (enveloped virus) Adenovirus (naked virus)

Virions• Diameter of virus

particle ranges from 20-200 nm (average 80 nm)

• Average diameter of bacterial cell is 1,000 nm

• Average diameter of eukaryotic cell is 10,000 nm

Retroviruses• RNA viruses• Uses Reverse Transcriptase enzyme to

copy RNA back to DNA• Causes a rapid mutation rate• Vaccine must be updated every year.

Viral Pathogenicity• Pathogenicity – ability to cause disease.

(infection)– depends upon the ability of the virus to infect its host– and the condition of host defense system.

Viruses have a specific host range. The host must have the target receptors or molecules.- range may be broad (specific class of organisms)Ex. rabies virus infects most mammals- range may be narrow (specific species)Ex. small pox virus infects humans only- range may be very narrow (specific cell line)Ex. Human immunodeficiency virus infects only helper T cells in

humans

• Certain hosts develop illness.• Certain hosts show no symptoms -

function as reservoirs.Ex. pigs & ducks serve as reservoirs for influenza (flu)

viruses.Influenza can jump from either animal to humans

(zoonosis).Mice serve as reservoirs for the Hantavirus. Mice will

remain healthy, humans that come in contact with saliva, urine or feces from the mice will become infected.

Viral Replication1. Attachment

– Attach to host cell by adhering to surface molecule2. Penetration

– Different methods – enzymes create hole, endocytosis3. Synthesis

– Host cell provides all resources and machinery– Viral DNA transcribed and translated by host ribosomes

4. Assembly– Capsid subunits join, genetic information packaged

5. Release– May burst cell or enveloped viruses bud from cell over

time• Damages or destroys host cell resulting in

disease• Time between infection and cell death varies

Lytic or lysogenic• Lytic infection (most viruses)

– Virus enters cell, immediately replicates, causes cell to lyse releasing new viruses

• Lysogenic– Virus enters cell– Inserts into host DNA as prophage– Remains latent without causing symptoms

• Copied along with host DNA into new cells– Some signal causes prophage to emerge and

revert back to the lytic stage.

Lysogenic StageSome viruses enter a period of dormancy after

invading a host cell this is called the latent period• integrate into the host chromosomes and are replicated

each time the cell divides• may alternate between periods of inactivity & recurrent

infections.• signal the host cell to replicate this may transform host

cell into a cancer cell.Ex. Herpesvirus & Epstein-Barr virus

Host defensesBacteria use restriction enzymes to destroy viral

DNA by chopping it to pieces.

Animal cells employ an immune system:• Antibodies coat viral particles so they can’t adhere to

target cells.• Certain virus-infected cells rupture before progeny

viruses can be released.• Virus-infected cells release chemicals that protect

surrounding uninfected cells.

Combating Viruses• Difficult• Once they infect the cells and incorporate their

DNA, our immune system can not identify them.• The cells replicate the viral DNA which results in a

cell line that is infected with viruses.• Very few anti-viral drugs and they are not very

affective• Once you get a virus you will always have the

virus.

Drugs• Antibiotics do not work against viruses• Difficult to develop drugs against viruses• Complicated by genetic variability of

viruses• Vaccination is our most potent weapon

– “Teach” immune system to recognize components of invader

– When the individual is exposed to the virus, the body recognizes it, and destroys it before it enters the cells.

– Smallpox and polio vaccinations highly effective

– Unable to develop vaccinations against all viruses

Other Infectious Agents1. Viroids - infectious RNAs that affect plants.

– Double stranded RNA, No protein coatEx. Avocado sunblotch, Tomato bunchy top, Chrysanthemum stunt disease

2. Prions – Proteinaceous infectious particle or PrP– They cause proteins to change shape (conformation)– Cascading effects– Infectious proteins associated with transmissible

spongiform encephalopathy that occurs in 80 different mammals.

– These are not detected by the immune system and will cause the cells to die.

Ex. Scrapie, Kuru, Creutzfeldt-Jakob disease, mad cow disease

Overview

BACTERIA AND ARCHAEA• We group these together as prokaryotes,

because they both lack a nucleus and any compartmentalization, but they are not very closely related based on DNA sequence.

• The Archaea is more closely related to Eukarya (Plants and Animals) than they are to bacteria.

Cladogram

• This information came from resent DNA sequence data

Bacteria Archaea Eukarya

Bacteria and Archaea Shared Characteristics• Both have a cell membrane• Both have ribosomes• Both have a nucleoid region that contains a

single circular chromosome• Both have a cell wall• Both are single celled organisms

Comparing Bacteria and

Archaean

Internal Structure

• DNA– One circular chromosome– Located in nucleoid (nuclear region)

• Plasmids – small circular pieces of DNA – Code for drug or toxin resistance, cause

disease, alter cell’s metabolism– Used in recombinant DNA technology– Accounts for most antibiotic resistance

• Ribosomes structurally different from eukaryotes and from each other– Some antibiotics exploit this difference– Ex. Streptomycin

Cell wall• Rigid structure outside cell membrane

– In bacteria it is composed of mainly Peptidoglycan

– In archaea it is composed of mainly pseudopeptidoglycan

• Gram stain differentiates between 2 major groups of bacteria which is based on cell wall structure– Gram-positive – appear purple due to thick

peptidoglycan layer– Gram-negative – appear pink due to thinner

cell walls and an outer membrane covering• Outer membrane is what causes the inflammation

response• 90-95% of these are harmful to their host

• Glycocalyx– Capsule or slime layer– Sticky layer outside cell wall– Attachment, resist drying,

protection from immune system• Pili

– Short, hair-like projections– Adhere to objects– Sex pili transfer DNA

• Flagellum– Whip-like extension to move cells– Not homologous to eukaryotic

flagella– Taxis – move toward or away from

stimulus– Ex: Chemotaxis, phototaxis,

geotaxis

• Endospores are thick walled structures that form around DNA & a small amount of cytoplasm.

• Allows bacteria to survive harsh conditions.

• Endospores can withstand boiling & drying.

• Can be killed by 10-15 minute superheated steam treatment. (Autoclaved)– Clostridium botulinum

• Botulism• Common in home canned foods due to improper

sterilization– Bacillus anthracis

• Anthrax

Classification• Traditionally relied on observable

characteristics– 3 common shapes – cocci (spherical), bacilli

(rod-shaped), and spirilla (spiral)– Cell arrangements – pairs, clusters (staphylo-),

or chains (strepto-)– Gram stain (positive or negative)– Other stains for flagella, endospores, or

glycocalyx

• Cocci - have spherical shaped cells

• Bacilli - have rod shaped cells

• Spirilla - have spiral shaped cells

• Based on Staining Characteristics• Gram positive (+) bacteria

Cell walls have thick peptidoglycan layer; stain purple.

• Gram negative (-) bacteria Cell walls have thin peptidoglycan layer & an outer membrane; stain pink.

Metabolic Pathways• Carbon source

– Autotrophs – acquire carbon from inorganic sources (CO2).– Heterotrophs – carbon from organic molecules

• Energy source– Phototroph – energy from the sun– Chemotroph – oxidize inorganic or organic chemicals

• Oxygen requirements– Obligate aerobe – requires oxygen

• Ex. Bacillus– Obligate anaerobe – oxygen is toxic

• Ex. Clostridium tetani– Facultative anaerobe – can live with or without oxygen

• Ex. Escherichia coli & Salmonella

Modern Methods of ClassificationBased on molecular data; groupings reflect

evolutionary relationships.Ribosomal RNA (rRNA) sequences of organisms

are compared to identify signature sequences.

Signature sequences are short stretches of nucleotides that are unique to certain types of organisms.

Molecular data show Bacteria and Archaeahave different:• genetic sequences and antibiotic sensitivities• cell wall components and membrane lipids• numbers of introns and repeated genetic sequences• cell shapes

Vertical Gene Transfer• Bacteria Reproduction• Use binary fission • Resembles mitosis; however, it is different

because it lacks spindle fibers & many types of proteins that are associated with the more complex linear chromosomes of eukaryotic cells.

• Chromosomes attaches to the cell membrane

Transformation

Transduction Conjugation

Domains• Domain Bacteria

– At least 23 phyla– Very diverse – photosynthetic, nitrogen cycling,

medically important, source of antibiotics• Domain Archaea

– “extremophiles” – first found in extremely hot, acidic, or salty environments

– More being discovered in moderate environments

– Often thought of as the most primitive– 3 phyla

• Only few species of bacteria are harmful to man because they are pathogenic. (1%)

• Bacterial infections may be spread by:• Air (inhalation)- Legionella pneumophila (causes

legionellosis, a form of pneumonia).• Arthropods (bites)- Yersinia pestis (causes bubonic

plague) is transmitted to humans by rat fleas.• Direct Contact - Neisseria gonorrhoeae (causes

gonorrhea) is transmitted by sexual contact.• Food & Water (ingestion)- Vibrio cholerae (causes

cholera); Salmonella enteritidis (causes food poisoning).

• Abrasions on the skin - Staphylococcus aureus

Harmful effects of Bacteria

Why they are harmful• Pili attach (anchor bacteria)

– Enzymes secreted destroy tissue.• Ex. Helicobacter pylori ( causes ulcers)

– Toxins produced destroy tissue.• Ex. Bacillus anthracis (causes anthrax)

Antibiotics• Inhibits cell wall production

– Penicillin• Disrupting cell membrane

– Polymyxin• Inhibits protein production (ribosomes)

– Erythromycin• Inhibits transcription (RNA polymerase)

– Rifamycin• Inhibits enzymes (metabolic pathways)

– Sulfanilamide

• Most prokaryotes are beneficial in that they:• break down organic wastes & dead

organisms.• cycle chemical elements (oxygen, nitrogen-

fixing) between organisms & the environment.

• are used in the production of food. (vinegar, pickles, sauerkraut, olives, yogurt, cheese)

• are used to mass-produce certain non- food items. (vitamins, enzymes, ethanol, acetone, human insulin & blood clotting factors)

• are used in water and waste treatment.• are used in bioremediation. (certain microbes

degrade oil, while others remove heavy metals from water)

Beneficial effects of Bacteria

Overview

Protists• The Kingdom Eukarya they are eukaryotes-meaning they

have a nucleus and membrane bound organelles.

• Multiple Kingdoms• Some are plant like they are autotrophic, contain

chloroplasts filled with chlorophyll. Ex. Algae and Euglena

• are aquatic• are heterotrophic and decompose Ex. Slime mold• are parasitic• Protozoans are another type of heterotrophic protist

some cause disease Ex. Trichomonas• Amoeba, Paramecium are examples• Basically any ekaryote not classified as Plant, Animal or

Fungi was classified as a Protists